The UK Fleming Fund: Developing microbiology laboratory capacity for AMR surveillance

Abstract

Background: The Fleming Fund is a UK Overseas Development Aid programme aiming to improve Antimicrobial Resistance (AMR) surveillance in low-and middle-income countries in Africa and Asia. The Fund has placed Country Grants in over 20 countries, to support implementation of the surveillance component of country AMR National Action Plans. Grants provide funding and technical assistance to develop AMR governance systems, and to improve country capacity for bacteriology diagnostics, AMR reporting and data analysis. In rolling out the programme, we have accumulated a substantial dataset on clinical microbiology capacity across a broad range of settings. Methods and materials: A standardised questionnaire was developed to assess the key laboratory components for bacterial culture, identification and antimicrobial susceptibility testing. The questionnaire addressed infrastructure, equipment, staff capacity, clinical reporting, and reporting into the National Surveillance System. The questionnaire was administered in laboratories to be supported by the Fleming Fund Country Grant programme. Results: Over 100 laboratories were assessed. The most common factors hindering delivery of diagnostic service were a lack of reliable power supply, unreliable consumable/reagent supply chains, budget constraints (either due to limited country budget for healthcare, or lack of dedicated laboratory budget within hospital funding mechanisms), and a lack of laboratory staff with specific microbiology training. We also identified a universal lack of clinical engagement with laboratory services, resulting in poor use of laboratories and a predominantly syndromic approach to management even where laboratory services were judged to be adequate. Conclusion: Clinical microbiology laboratory capacity was extremely limited across the sites and countries assessed, meaning that most cases of infection in these countries are managed in the absence of any reliable microbiology data to inform individual treatment or empiric guidelines. The Fleming Fund aims to improve capacity through the Grant programme, but additional solutions are needed to ensure that efforts to improve use of antimicrobials as part of the global response to AMR are supported by adequate laboratory services. Clinician engagement is urgently needed to drive demand for better services and data, in conjunction with laboratory investment to break the vicious spiral of unreliable results, poor trust, reduced sample throughput and further lowering of quality.